A large genome center's improvements to the Illumina sequencing system

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The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the quantity of purity-filtered sequence data generated by our Genome Analyzer (Illumina) platforms reached 1 terabase, and our average weekly Illumina production output is currently 64 gigabases. Here we describe a set of improvements we have made to the standard Illumina protocols to make the library preparation more reliable in a high-throughput environment, to reduce bias, tighten insert size distribution and reliably obtain high yields of data.

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Figure 1: Illumina sequencing workflow.
Figure 2: Sample fragmentation.
Figure 3: A-tailing, ligation and size selection.
Figure 4: PCR.
Figure 5: Quantification.
Figure 6: Denaturation.


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We thank all the staff at Illumina for their support, particularly T. Ost, M. Gibbs, J. Smith, N. Gormley, V. Smith and K. Hall. We also thank C. Brown, A. Brown, R. Pettett, T. Skelly, N. Whiteford, L. Mamanova, E. Sheridan and E. Huckle for helpful discussions and assistance.

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Correspondence to Daniel J Turner.

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Competing interests

H.S. is an Illumina shareholder and share option holder.

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Supplementary Table 1 , Supplementary Protocols 1–13 (PDF 110 kb)

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